The Evolution of the Autoimmune Protocol

What the New Research Means for You

The Autoimmune Protocol (AIP) has always been more than a diet. It’s a therapeutic framework designed to reduce inflammation, support gut and immune health, and create space for healing in people navigating autoimmune disease.

Recently, Nutritional Therapy Practitioner, Chef, and respected author Mickey Trescott shared important news: the release of updated research and an evolved approach to AIP, which now includes what is referred to as Modified AIP.

This evolution reflects years of clinical observation, emerging research, and a deeper understanding of how diverse autoimmune journeys truly are.

So what does this mean for you?

Let’s break it down.

Why AIP Is Evolving

When AIP was first formalized, the core elimination phase served a critical purpose:
to create a low-inflammatory, low-reactivity baseline for individuals with complex immune systems.

Over time, practitioners and researchers began to notice important patterns:

Some individuals experienced symptom improvement without needing full elimination
Others benefited from earlier or more flexible inclusion of certain foods
Long-term restriction was not always necessary — or appropriate — for everyone

New research supports what many clinicians have observed in practice: there is no single path to healing.

The modified AIP was developed to reflect this reality, offering a more flexible, individualized approach for those who may be more stable, well supported, or further along in their healing journey.

Core AIP vs. Modified AIP: What’s the Difference?

Both Core AIP and Modified AIP share the same foundational principles:

Nutrient density
Whole, unprocessed foods
Support for gut and immune health
Lifestyle foundations such as sleep, stress management, connection and movement

The difference lies in how much flexibility is appropriate, and when.

Core AIP remains the most comprehensive elimination approach, removing foods most strongly associated with immune activation, gut permeability, and inflammation.

Modified AIP allows for the inclusion of additional food categories when appropriate, based on symptom stability, tolerance, and individual context.

What Foods Are Included on Modified AIP?

Modified AIP is designed to be a more flexible and sustainable approach within the AIP framework, while still avoiding foods most consistently associated with immune activation.

Rather than a single rigid food list, Modified AIP reflects emerging research and clinical experience showing that some individuals do not require full core elimination to experience meaningful symptom improvement.

Foods Commonly Included on Modified AIP

Grains & Pseudo-Grains (Context-Dependent)
Modified AIP may include select gluten-free grains and pseudo-grains, such as:

White and brown rice
Quinoa
Buckwheat
Amaranth
Chia

These are typically considered when digestive symptoms are stable and immune activity is well managed.

Legumes (Excluding Soy & Peanuts)
Many legumes may be included, including:

Beans
Lentils
Chickpeas

Soy and peanuts remain excluded due to their stronger association with immune reactivity.

Seeds & Seed-Based Products
Unlike core AIP, Modified AIP may allow:

Flaxseed
Sunflower seeds
Coffee
Cocoa and dark chocolate

Tolerance varies widely, and portion size and frequency matter.

Fats

Ghee (clarified butter) is included, as it removes most milk proteins found in dairy.

Who Modified AIP May Be Best Suited For

Modified AIP is often used:

As a starting point for individuals new to AIP
By those who did not require full core elimination to see improvement
When sustainability, affordability, or quality of life is a key concern

For individuals navigating active flares, complex autoimmune conditions, or high food sensitivity, core AIP may still provide the most supportive therapeutic foundation.

Modified AIP is about personalization — not shortcuts.

What about Urban AIP Meals?

At Urban AIP, we’ve chosen to continue preparing 100% core AIP-compliant meals — not because we oppose Modified AIP, but because our mission is to serve the widest possible range of autoimmune needs.

By staying fully core-AIP compliant, we ensure that:

Elimination-phase customers can order with confidence
Those in active flares have safe, reliable options
Practitioners can broadly recommend our meals
Customers following Modified AIP can layer in flexibility on their own terms

Our goal remains to remove stress, guesswork, and food anxiety, no matter where you are in your healing journey.

Learn More: Mickey Trescott’s New Book

For those who want to explore the research and clinical reasoning behind Modified AIP in greater depth, and discover exciting new recipes, Mickey Trescott’s upcoming book offers a thoughtful, science-informed perspective on how AIP continues to evolve and of course, invites you to try Mickey’s outstanding recipes as always.

👉 [Pre-order Mickey Trescott’s book here]

We deeply respect Mickey’s contributions to the AIP community and are grateful to see the protocol continue to grow in a way that honors both science and lived experience.

The future of AIP isn’t about rigid rules — it’s about informed choice, compassionate care, and individualized healing.

Frequently Asked Questions

FAQ 1: How is the Autoimmune Protocol different today than when it was first introduced?

Answer:

The Autoimmune Protocol has evolved significantly since its early days. While the original approach focused heavily on strict elimination, today’s AIP emphasizes personalization, nutrient density, stress management, sleep, and a thoughtful reintroduction phase. Modern AIP also recognizes that healing is not linear and that long-term success comes from flexibility, sustainability, and identifying individual triggers rather than remaining in elimination indefinitely.

FAQ 2: Is the Autoimmune Protocol still considered relevant for autoimmune healing?